[English] 日本語
Yorodumi- PDB-1gcy: HIGH RESOLUTION CRYSTAL STRUCTURE OF MALTOTETRAOSE-FORMING EXO-AMYLASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gcy | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF MALTOTETRAOSE-FORMING EXO-AMYLASE | ||||||
Components | GLUCAN 1,4-ALPHA-MALTOTETRAHYDROLASE | ||||||
Keywords | HYDROLASE / BETA-ALPHA-BARREL / BETA SHEET | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotetraohydrolase / glucan 1,4-alpha-maltotetraohydrolase activity / starch catabolic process / starch binding / alpha-amylase activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mezaki, Y. / Katsuya, Y. / Kubota, M. / Matsuura, Y. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2001 Title: Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri. Authors: Mezaki, Y. / Katsuya, Y. / Kubota, M. / Matsuura, Y. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Crystal Structure of a Maltotetraose-forming Exo-amylase from Pseudomonas stutzeri Authors: Morishita, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M. / Sakai, S. #2: Journal: J.Mol.Biol. / Year: 1997 Title: Crystal Structure of a Mutant Maltotetraose-forming Exo-amylase Cocrystallized with Maltopentaose Authors: Yoshioka, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gcy.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gcy.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 1gcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gcy_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gcy_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 1gcy_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1gcy_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gcy ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gcy | HTTPS FTP |
-Related structure data
Related structure data | 2amgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57769.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: MO-19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P13507, glucan 1,4-alpha-maltotetraohydrolase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | The C-terminal raw-starch binding domain of about a hundred amino acids is disordered in the crystal. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.52 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.834 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. obs: 66492 / % possible obs: 89.6 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.061 |
Reflection | *PLUS Num. measured all: 222219 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AMG Resolution: 1.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|